Results for "Multiple Sequence Alignment Algorithms"
Bio-Scripts
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -qu...| efetch -format fasta > seq2.fa #fastANI for alignment free comparision #conda inst...seq2.fa --visualize -o fastani.out #Plot using sequences...1125 days ago
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #...1125 days ago
BioPerl to convert between sequence formats from Fasta to Genbank
#!/usr/local/bin/perl -w # Sequence formats to choose: Fasta, EMBL. GenBank, Swissprot, PIR and GCG use Bio::SeqIO; $inFile = "BRCA2.fa"; $in = Bio::SeqIO->n...2940 days ago
- #!/usr/local/bin/perl -w # Can be easily modified to run any command on every sequence in a folder # Directory of sequences $myDir = "/home/anjana/seqs";...file $patFile = "/home/anjana/patterns/polyA.pat"; # Go to sequence d...
2940 days ago
- #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT"; my $polyA = "AAAA"; #concatenate two strings my $modifiedDNA = $...
2941 days ago
Count the frequency of base G in a given DNA sequence
#!/usr/bin/perl use strict; use warnings; my $DNA = "GATTACACAT"; #initialize $countG...lculate the length of $DNA my $DNAlength = length($DNA); #for each letter in the sequence c...2941 days ago
- #!/usr/bin/perl use strict; use warnings; my $DNA = "GATTACACAT"; #tra...A = $DNA; $RNA =~ s/T/U/g; print "RNA sequence is $RNA\n"; #find the reve...titution operator #first - reverse the sequence...nslation operator #first - reverse the sequence...
2941 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die...print "GI: $2\n"; } elsif (/(DEFINITION\s*)(.*)(\.)/) { print "Sequence n...2941 days ago
Perl script to Mutate a DNA Sequence
#!/usr/local/bin/perl -w # This script randomly mutates the DNA sequence and generates 10 successive mutation results. #...this script it asks for the file name of the DNA sequence....ndows: c:\rnafile.txt # In Linux : /home/user/sequence/r...2940 days ago
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
#!/usr/local/bin/perl -w # While executing this script it asks for the file name of the DNA sequence. If the sequence file is not available in the same...he path. In windows: c:\dnafile.txt, In Linux: /home/user/sequence/d...2940 days ago
